Fig. 4: eRNAs form an extensive interaction network with the N-terminal region of NELF-E and the tentacles of NELF-A and NELF-E.

a The bar plot visualizes the total number of protein–RNA crosslinks (total count of nseen) to each NELF subunit for four (out of eight) eRNA crosslinking experiments to the isolated NELF complex and for two (out of two) experiments with the entire PEC (Supplementary Fig. 4a, experiments marked in red; Supplementary Data 4–7). Below is a 10% SDS-PAGE of two crosslinking experiments of 4SU-labeled Nr4a1-(a) eRNAs 1–100, before (−) and after (+) 365 nm-induced crosslinking to the NELF complex is shown. 40% and 80%-4SU denote the concentration of 4-thiouridine vs. uridine during in vitro transcription (Supplementary Fig. 4a, Methods). Upon crosslinking predominantly NELF-E and NELF-A disappears while high-molecular bands corresponding to crosslinked protein–RNA products appear (marked by red asterisks). b Total number of nucleotide-crosslinks at each amino acid (aa) position plotted along the NELF-E sequence (1–380 aa). Data were shown for the same samples as in (a). The crosslinking results for all eight experiments are shown in Supplementary Fig. 5. Clusters of crosslinks or single crosslinking positions that are present throughout all samples are highlighted. Representative amino acid residues are indicated above the highlighted boxes. The domain architecture of NELF-E is schematically displayed on top. c Distribution of all crosslinks plotted in (b) between the N-terminal portion of NELF-E and the NELF-E tentacle. d Nucleotide-crosslinks to NELF-A plotted as in (b). e Distribution of all crosslinks plotted in (d) between the NELF-AC lobe and the NELF-A tentacle. f Nucleotide-crosslinks to the NELF-AC lobe mapped onto the PEC (PDB code 6GML) displayed in the left panel. Crosslinked residues in the vicinity of the positively charged patches 4 (middle panel) and 1–3 (right panel) are displayed as sticks and colored in yellow. The referring amino acid is reported next to the structure and in the color of the corresponding NELF subunit (NELF-A = orange; NELF-C = blue). Lysine and arginine residues associated with the positively charged patches⁴² are also shown as sticks and colored in black. T157 is highlighted in pink and marked with an encircled P. Source data for (a, c, e) are provided in a Source Data file. Data shown in (b, d) are part of Supplementary Data 4, 6.